Real-time modelling with EpiNow2
Example applications


Sebastian Funk (@sbfnk)
https://epiforecasts.io

12 December, 2022
100 days and 100 lines of code

“We were losing ourselves in details […] all we needed to know is, are the number of cases rising, falling or levelling off?”

Hans Rosling, Liberia, 2014

Infections are reported with a delay

UKHSA, 2022

Data contain noise and reporting artefacts

Epidemics grow exponentially

EpiNow2

An R package for situational assessment in outbreaks taking into account

  • reporting delays and truncation
  • reporting artefacts such as week-day effects
  • exponential nature of epidemics

EpiNow2


and many contributions from people that don’t show up in code

EpiNow2

https://epiforecasts.io/EpiNow2
Abbott et al., Wellcome Open Res, 2020

Application: COVID-19

https://epiforecasts.io/covid
https://epiforecasts.io/posts/2022-03-25-rt-reflections

Application: Monkeypox nowcasting

https://github.com/epiforecasts/nowcasting.example

Application: Cholera in Haiti

Future development: flexible nowcasting

https://package.epinowcast.org/dev/

  • Outbreak modelling has common tasks
  • Methods usually chosen for availability
  • Much scope for improving
    • software,
    • methodology and
    • practices